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FLS > Structure and replication of DNA > Flashcards

Structure and replication of DNA Flashcards

1
Q

What is a nucleotide?

A

It has:
A 5-carbon sugar deoxyribose
A nitrogen containing base attached to the sugar.
A phosphate group

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2
Q

What does a nucleotide look like?

A

Label the components and the bonds

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3
Q

What is a nucleoside?

A

Sugar and base.

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4
Q

What is a glycosidic bond?

A

N-glycosidic bond is between the sugar and the nitrogenous base and provides stability.

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5
Q

What is the difference between a nucleoside and a nucleotide?

A

A nucleoside becomes a nucleotide when phosphate is bonded to the 5’ carbon of 2-deoxyribose, using a phosphodiester bond.

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6
Q

What is a phosphodiester bond?

A

A phosphodiester bond is between the 5’ carbon sugar and phosphate.

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7
Q

What is the direction of polynucleotide strands?

A

5’-3’ direction, irrespective of which strand.

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8
Q

How do nucleotide strands bind to each other?

A

Hydrogen bonding between adjacent nitrogenous base pairs.
Thymine and adenine have 2 hydrogen bonds.
Guanine and cytosine have 3 hydrogen bonds.

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9
Q

What is the characteristic of hydrogen bonding?

A

Hydrogen bonding gives stability of polynucleotide chains running anti-parallel to each other.
As the guanine and cytosine pairing have more hydrogen bonds, they are more stable.

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10
Q

What does adenine and thymine base pairing look like?

A
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11
Q

What does guanine and cytosine base pairing look like?

A
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12
Q

What is the difference between a purine and a pyrimidine?

A

Purines have 2 rings - adenine and guanine.
Pyrimidines have 1 ring - thymine and cytosine.

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13
Q

How are the base pairings unusual?

A

Despite adenine and thymine having 2 hydrogen bonds, and guanine and cytosine having 2, they take up the same space in the nucleus.

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14
Q

How does hydrogen bonding affect the structure of DNA?

A

Hydrogen bonding between bases allows a twist to the anti-parallel structure so there is a double helix.
The helix twists and so the large amount of information needed is compacted so it can be unravelled, allowing eukaryotic processes to take place.

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15
Q

Which groups are attached to which carbons of the deoxyribose sugar?

A

The nitrogenous base is attached to 1’ carbon.
Phosphate group is 5’.
A hydroxyl (OH) group is attached to 3’, allowing subsequent nucleotides to be bound.

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16
Q

What is the structure of the DNA double helix?

A

The phosphate groups are on the outside, and the bases are in the middle, so a helix can form.
This forms major and minor grooves.

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17
Q

What is the importance of grooves?

A

They allow eukaryotic processes to take place.
Transcription factors or replication machineries can bind to major or minor grooves.
They allow exposure of DNA to these important factors.

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18
Q

How do phosphodiester bonds form?

A

Replication by condensation reaction forms a phosphodiester bond between the phosphate and sugar.

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19
Q

How do adjacent nucleotides join?

A

The 3’ hydroxyl group on the sugar forms an ester bond to the 5’ phosphate group.

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20
Q

What are the requirements for DNA division?

A

When a cell divides, both daughter cells must receive a complete set of genes, so the chromosomes must replicate accurately before division.

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21
Q

What is the process of asexual replication in prokaryotes?

A

The entire genome is on one circular chromosome.
The chromosome replicates once to produce two chromosomes that are identical.
The identical daughter chromosomes move to opposite ends of the cell.
When the cell divides the daughter chromosomes are partioned to each daughter cell.

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22
Q

What are the phases of the cell cycle?

A

Mitosis –> Gap phase 1 –> S phase –> Gap 2 phase

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23
Q

What happens in the S phase of the cell cycle?

A

DNA replicates.

24
Q

What happens in the gap phases of cycle?

A

Gene expression occurs in G1 and G2.
Some genes are expressed in the S phase, but these are not highly expressed genes.

25
Q

At what point are differently expressed genes replicated?

A

Highly expressed genes are replicated early in S phase.
Silent genes are replicated late.

26
Q

What are the 2 final stages of mitosis?

A

Nuclear division occurs during mitosis.
Cell division / cytokinesis occurs at the end of mitosis.

27
Q

What are the features of DNA replication?

A

Semi conservative
Bidirectional
Proceeds from the origin
5’-3’ direction
High degree of fidelity
Multi enzymatic process

28
Q

What are the stages of DNA replication?

A

Initiation
Elongation
Termination

29
Q

Why is DNA replication semi-conservative?

A

The strands separate
A new strand is made using each old strand as a template by base pairing.

30
Q

What is the order of enzymatic activity in DNA replication?

A

Helicase, single-strand binding protein, primase

31
Q

What does helicase do?

A

Helicase unwinds double-helical DNA, by breaking hydrogen bonds between base pairs.

32
Q

What do single-strand binding proteins do?

A

SSB protein binds to and stabilises the single strand to keep DNA bound.

33
Q

What does primase do?

A

Primase adds ribonucleoside triphosphates (dNTPs) to synthesise an RNA primer. Polymerase can then bind to the primer and begin replication.
Primase binds at the initiation point of the 3’-5’ parent chain.

34
Q

What is DNA polymerase?

A

Removes RNA primers from the lagging strand and replaces them with DNA nucleotides.

35
Q

What is DNA polymerase III?

A

DNA pol III attaches to the 3’ end of the primer and covalently joins free nucleotides in a 5’-3’ direction.

36
Q

What is the direction of DNA polymerase III?

A

The strands are antiparallel so moves in opposite directions on the strands.
On the leading strand it moves towards the replication fork and synthesises continuously.
On the lagging strand, DNA pol is moving away from the fork and synthesis in Okazaki fragments.

37
Q

What are the characteristics of DNA polymerase?

A

5’-3’ direction.
Requires all 4 dNTPs.
Must have a template and a primer.
Has proof reading activity.

38
Q

How does DNA polymerase have proof reading activity?

A

It reads the parent strand, lays down the complementary base, then returns and checks the right bases are laid down.
This ensure fidelity.

39
Q

What is a-polymerase?

A

Synthesises the RNA primer, initates DNA synthesis and lagging strand.
Has no exonuclease activity.

40
Q

What is b-polymerase?

A

Repairs DNA
No exonuclease activity.

41
Q

What is y-polymerase?

A

Replicates mitochondrial DNA.
3’-5’ exonuclease activity.

42
Q

What is S-polymerase?

A

Synthesises leading strand, fills DNA gaps after primer removed.
3’-5’ exonuclease activity.

43
Q

What is E-polymerase?

A

Repairs DNA.
3’-5’ exonuclease activity.

44
Q

What are exonucleases?

A

Removes nucleotides from the end of a DNA strand.
Different types of exonuclease enzymes work 5’-3’ or 3’-5’.

45
Q

What is ligase?

A

Ligase joins end of single DNA strands (Okazaki fragments) by covalently joining sugar-phosphate backbones together with phosphodiester bonds.

46
Q

How does an exonuclease remove RNA primer?

A

RNA primer contains ribose instead of 2-deoxyribose, so exonucleases can identify it and removes it.

47
Q

What is the origin of replication?

A

A replication fork with two strands of DNA running in antiparallel directions.
In prokaryotes there is only one origin of replication.
In eukaryotes there are multiple.

48
Q

What is the leading strand?

A

The leading strand can continuously replicate as helicase is in front of it unwinding the helix.

49
Q

What is the lagging strand?

A

The lagging strand is replicated at the same time as the leading, but has to wait for helicase to break down the hydrogen bonds before it can lay down RNA primer for the DNA polymerase to bind and replicate.
It is made up of small Okazaki fragments.

50
Q

What does the replication fork look like?

A
51
Q

What is the significance of eukaryotes having multiple origins of replication?

A

Bases are added at a rate of 100/second.
So replication of the whole mammalian genome takes approximately 8 hours. The cell cycle is 16-18 hours.

52
Q

How do the multiple origins of replication in eukaryotes join?

A

They are bidirectional at each point on the strands, so bubbles form which flatten out at the end and join, forming a continuum of DNA.

53
Q

What is gyrase?

A

A topoisomerase, it relaxes supercoils, via negative supercoiling, produced when the molecule is twisted during replication.

54
Q

What is telomerase?

A

It uses a short RNA template to add short DNA repeats to the short ends of linear chromosomes when the last primer is removed using RNA template.

55
Q

What are telomeres?

A

Telomeres are found at the linear end of DNA and are guanine and cytosine rich repeats.
They are highly conserved and essential to maintain the integrity of DNA.

56
Q

What does telomerase do?

A

Telomerase replicates telomers.
Every replication the telomers loses 10-15 bases.
So older people have shorter telomers and are more at risk as the genome is less protected.

57
Q

What is the diagram of enzymes and things in replication?

A

FLS (14 decks)

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